[Bioperl-l] GenBank ASN.1 SeqIO parser

Ryan Golhar golharam at umdnj.edu
Thu Feb 7 18:00:33 EST 2008


That I can use from Perl?  Such as????


I need to retrieve Gene Ontology information (classification and GO id) 
from the Entrez Gene record.  I thought it would be easiest using 
BioPerl to do this.  BioPerl only has an ASN.1 parser, entrezgene.

When I use this to load the Gene record, I'm using:

my $io = Bio::SeqIO->new(-file => '</tmp/gene.asn', -format => 
"entrezgene" );
my $seq_obj = $io->next_seq;


Something is not working with the second line.  I get an error:

  "Use of uninitialized value in string eq at
         /home/golharam/bioperl/bioperl-1.5.1//Bio/SeqIO/entrezgene.pm 
line 244"

It sort of makes sense because, well, the Entrez Gene record doesn't 
have a sequence...it has information about a gene.

I figure I must be doing something wrong but I haven't seen anything in 
BioPerl about parsing entrez gene records any other way.

Ryan


Jason Stajich wrote:
> ugh - why parse ASN.1? NCBI provides converter application in the ncbi 
> toolkit to many formats : genbank, XML, etc.
> On Feb 7, 2008, at 1:48 PM, Chris Fields wrote:
> 
>> No.  The only ASN.1 parser is entrezgene.  You could probably try 
>> building one using the same ASN.1 parser that SeqIO::entrezgene uses 
>> (Bio::ASN1::EntrezGene); it includes a parser for sequences:
>>
>> http://search.cpan.org/~mingyiliu/Bio-ASN1-EntrezGene-1.091/lib/Bio/ASN1/Sequence.pm 
>>
>>
>> chris
>>
>> On Feb 7, 2008, at 3:24 PM, Ryan Golhar wrote:
>>
>>> Is there a SeqIO parser module for GenBank ASN.1 format?  I thought 
>>> it would have been genbank or entrezgene, but neither of them work.
>>>
>>> _______________________________________________
>>> Bioperl-l mailing list
>>> Bioperl-l at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
>>
>> Christopher Fields
>> Postdoctoral Researcher
>> Lab of Dr. Robert Switzer
>> Dept of Biochemistry
>> University of Illinois Urbana-Champaign
>>
>>
>>
>> _______________________________________________
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>> Bioperl-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioperl-l
> 
> 
> 



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